diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index ebdd4a86cf6e2c39de9dca641bb0e04013815979..0fa57e1cb497d584126a93a1927032e53c872e6c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -580,38 +580,132 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
Map<SampleOwnerIdentifier, SampleOwner> sampleOwnerCache)
{
assert sampleIdentifiers != null : "Sample identifiers unspecified.";
- Map<SampleOwner, List<String>> samplesByOwner = new HashMap<SampleOwner, List<String>>();
+
+ Map<SampleOwnerWithContainer, List<String>> samplesByOwner =
+ new HashMap<SampleOwnerWithContainer, List<String>>();
for (SampleIdentifier sampleIdentifier : sampleIdentifiers)
{
final SampleOwner sampleOwner = getSampleOwner(sampleOwnerCache, sampleIdentifier);
- List<String> ownerSamples = samplesByOwner.get(sampleOwner);
+ final String containerCodeOrNull = sampleIdentifier.getContainerCodeOrNull();
+ final SampleOwnerWithContainer owner =
+ new SampleOwnerWithContainer(sampleOwner, containerCodeOrNull);
+
+ List<String> ownerSamples = samplesByOwner.get(owner);
if (ownerSamples == null)
{
ownerSamples = new ArrayList<String>();
- samplesByOwner.put(sampleOwner, ownerSamples);
+ samplesByOwner.put(owner, ownerSamples);
}
- ownerSamples.add(sampleIdentifier.getSampleCode());
+ ownerSamples.add(sampleIdentifier.getSampleSubCode());
}
final ISampleDAO sampleDAO = getSampleDAO();
final List<SamplePE> results = new ArrayList<SamplePE>();
- for (Entry<SampleOwner, List<String>> entry : samplesByOwner.entrySet())
+ for (Entry<SampleOwnerWithContainer, List<String>> entry : samplesByOwner.entrySet())
{
- SampleOwner sampleOwner = entry.getKey();
- List<String> sampleCodes = entry.getValue();
+ final SampleOwnerWithContainer owner = entry.getKey();
+ final List<String> sampleCodes = entry.getValue();
+
+ final SampleOwner sampleOwner = owner.getSampleOwner();
+ final String containerCodeOrNull = owner.getContainerCodeOrNull();
+
List<SamplePE> samples = null;
if (sampleOwner.isDatabaseInstanceLevel())
{
samples =
- sampleDAO.listByCodesAndDatabaseInstance(sampleCodes,
+ sampleDAO.listByCodesAndDatabaseInstance(sampleCodes, containerCodeOrNull,
sampleOwner.tryGetDatabaseInstance());
} else
{
assert sampleOwner.isGroupLevel() : "Must be of space level.";
- samples = sampleDAO.listByCodesAndGroup(sampleCodes, sampleOwner.tryGetGroup());
+ samples =
+ sampleDAO.listByCodesAndGroup(sampleCodes, containerCodeOrNull,
+ sampleOwner.tryGetGroup());
}
results.addAll(samples);
}
return results;
}
+
+ /** Helper class encapsulating {@link SampleOwner} and code of container of a sample. */
+ private static class SampleOwnerWithContainer
+ {
+ private final SampleOwner sampleOwner;
+
+ private final String containerCodeOrNull;
+
+ public SampleOwnerWithContainer(SampleOwner sampleOwner, String containerCodeOrNull)
+ {
+ assert sampleOwner != null;
+ this.sampleOwner = sampleOwner;
+ this.containerCodeOrNull = containerCodeOrNull;
+ }
+
+ public SampleOwner getSampleOwner()
+ {
+ return sampleOwner;
+ }
+
+ public String getContainerCodeOrNull()
+ {
+ return containerCodeOrNull;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result =
+ prime * result
+ + ((containerCodeOrNull == null) ? 0 : containerCodeOrNull.hashCode());
+ result = prime * result + sampleOwner.hashCode();
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (!(obj instanceof SampleOwnerWithContainer))
+ {
+ return false;
+ }
+ SampleOwnerWithContainer other = (SampleOwnerWithContainer) obj;
+ if (containerCodeOrNull == null)
+ {
+ if (other.containerCodeOrNull != null)
+ {
+ return false;
+ }
+ } else if (!containerCodeOrNull.equals(other.containerCodeOrNull))
+ {
+ return false;
+ }
+ if (!sampleOwner.equals(other.sampleOwner))
+ {
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "SampleOwnerWithContainer [sampleOwner=" + sampleOwner
+ + ", containerCodeOrNull=" + containerCodeOrNull + "]";
+ }
+
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index 15eeecb5c8206fe3088948a675fe29ebf2cdb7e6..7b3b58b875ba85f46cf8187eaf8e5abc42df2c48 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -239,6 +239,7 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
batchUpdateProperties(sample, updates.getProperties(), details.getPropertiesToUpdate());
checkPropertiesBusinessRules(sample, propertiesCache);
+ // TODO 2010-10-09, Piotr Buczek: don't check business rules if value wasn't changed
if (details.isExperimentUpdateRequested())
{
updateGroup(sample, updates.getSampleIdentifier(), sampleOwnerCache);
@@ -325,27 +326,13 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
Map<SampleOwnerIdentifier, SampleOwner> sampleOwnerCache)
{
final List<SamplePE> results = new ArrayList<SamplePE>();
- List<SampleIdentifier> identifiersToLoadInBatch = new ArrayList<SampleIdentifier>();
+ List<SampleIdentifier> identifiers = new ArrayList<SampleIdentifier>();
for (SampleBatchUpdatesDTO sampleUpdates : updates)
{
SampleIdentifier identifier = sampleUpdates.getOldSampleIdentifierOrNull();
- if (identifier.getSampleCode().contains(
- SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING))
- {
- // contained samples can't be loaded in batch
- SamplePE sample = tryToGetSampleByIdentifier(identifier);
- if (sample == null)
- {
- throw UserFailureException.fromTemplate(
- "No sample could be found with given identifier '%s'.", identifier);
- }
- results.add(sample);
- } else
- {
- identifiersToLoadInBatch.add(identifier);
- }
+ identifiers.add(identifier);
}
- results.addAll(listSamplesByIdentifiers(identifiersToLoadInBatch, sampleOwnerCache));
+ results.addAll(listSamplesByIdentifiers(identifiers, sampleOwnerCache));
return results;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
index 004d07d072f09b54eff78e2d5d2671eeaf31c8b8..a43dd770fbde8975eda5f01ec03874bbcb7531e5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
@@ -54,9 +54,12 @@ public interface ISampleDAO extends IGenericDAO<SamplePE>
/**
* Returns a list of samples with given <var>databaseInstance</var> and one of given codes.
+ *
+ * @param containerCodeOrNull if specified all returned samples should have container with
+ * specified code, otherwise they shouldn't have any container
*/
List<SamplePE> listByCodesAndDatabaseInstance(final List<String> sampleCodes,
- final DatabaseInstancePE databaseInstance);
+ String containerCodeOrNull, final DatabaseInstancePE databaseInstance);
/**
* Returns the sample specified by given <var>sampleCode</var> and given <var>group</var>.
@@ -66,8 +69,12 @@ public interface ISampleDAO extends IGenericDAO<SamplePE>
/**
* Returns a list of samples with given <var>group</var> and one of given codes.
+ *
+ * @param containerCodeOrNull if specified all returned samples should have container with
+ * specified code, otherwise they shouldn't have any container
*/
- List<SamplePE> listByCodesAndGroup(final List<String> sampleCodes, final GroupPE group);
+ List<SamplePE> listByCodesAndGroup(final List<String> sampleCodes, String containerCodeOrNull,
+ final GroupPE group);
/**
* Inserts given list of {@link SamplePE} into the database in one go.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
index e1e8090b4521d3cf119b8d5b152c5fe85f43a3eb..29f43837fb8767712f9063a7eeb8e8b9b4573569 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
@@ -207,13 +207,13 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
}
public final List<SamplePE> listByCodesAndDatabaseInstance(final List<String> sampleCodes,
- final DatabaseInstancePE databaseInstance)
+ final String containerCodeOrNull, final DatabaseInstancePE databaseInstance)
{
assert sampleCodes != null : "Unspecified sample codes.";
assert databaseInstance != null : "Unspecified database instance.";
Criteria criteria = createDatabaseInstanceCriteria(databaseInstance);
- addSampleCodesCriterion(criteria, sampleCodes);
+ addSampleCodesCriterion(criteria, sampleCodes, containerCodeOrNull);
List<SamplePE> result = cast(criteria.list());
if (operationLog.isDebugEnabled())
{
@@ -245,13 +245,13 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
}
public final List<SamplePE> listByCodesAndGroup(final List<String> sampleCodes,
- final GroupPE group)
+ final String containerCodeOrNull, final GroupPE group)
{
assert sampleCodes != null : "Unspecified sample codes.";
assert group != null : "Unspecified space.";
Criteria criteria = createGroupCriteria(group);
- addSampleCodesCriterion(criteria, sampleCodes);
+ addSampleCodesCriterion(criteria, sampleCodes, containerCodeOrNull);
List<SamplePE> result = cast(criteria.list());
if (operationLog.isDebugEnabled())
{
@@ -267,7 +267,7 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
private SamplePE tryFindContainedSampleWithUniqueSubcode(Criteria criteria, String sampleCode)
{
- addContainedSampleCodeCriterion(criteria, sampleCode);
+ addContainedCodeCriterion(criteria, sampleCode);
List<SamplePE> list = cast(criteria.list());
return list.size() == 1 ? list.get(0) : null;
}
@@ -290,32 +290,41 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
return createFindCriteria(Restrictions.eq("group", group));
}
- private void addSampleCodesCriterion(Criteria criteria, List<String> sampleCodes)
+ private void addSampleCodesCriterion(Criteria criteria, List<String> sampleCodes,
+ String containerCodeOrNull)
{
- // no support for contained samples
- criteria.add(Restrictions.in("code", sampleCodes));
- criteria.add(Restrictions.isNull("container"));
+ List<String> convertedCodes = new ArrayList<String>();
+ for (String sampleCode : sampleCodes)
+ {
+ convertedCodes.add(CodeConverter.tryToDatabase(sampleCode));
+ }
+ criteria.add(Restrictions.in("code", convertedCodes));
+ addSampleContainerCriterion(criteria, containerCodeOrNull);
}
- private void addSampleCodeCriterion(Criteria criteria, String sampleCode)
+ private void addSampleContainerCriterion(Criteria criteria, String containerCodeOrNull)
{
- String[] sampleCodeTokens =
- sampleCode.split(SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING);
- if (sampleCodeTokens.length > 1)
+ if (containerCodeOrNull != null)
{
- final String containerCode = sampleCodeTokens[0];
- final String code = sampleCodeTokens[1];
- criteria.add(Restrictions.eq("code", CodeConverter.tryToDatabase(code)));
criteria.createAlias("container", "c");
- criteria.add(Restrictions.eq("c.code", CodeConverter.tryToDatabase(containerCode)));
+ criteria.add(Restrictions.eq("c.code", CodeConverter.tryToDatabase(containerCodeOrNull)));
} else
{
- criteria.add(Restrictions.eq("code", CodeConverter.tryToDatabase(sampleCode)));
criteria.add(Restrictions.isNull("container"));
}
}
- private void addContainedSampleCodeCriterion(Criteria criteria, String sampleCode)
+ private void addSampleCodeCriterion(Criteria criteria, String sampleCode)
+ {
+ String[] sampleCodeTokens =
+ sampleCode.split(SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING);
+ String subCode = sampleCodeTokens.length > 1 ? sampleCodeTokens[1] : sampleCode;
+ String containerCodeOrNull = sampleCodeTokens.length > 1 ? sampleCodeTokens[0] : null;
+ criteria.add(Restrictions.eq("code", CodeConverter.tryToDatabase(subCode)));
+ addContainedCodeCriterion(criteria, containerCodeOrNull);
+ }
+
+ private void addContainedCodeCriterion(Criteria criteria, String sampleCode)
{
criteria.add(Restrictions.eq("code", CodeConverter.tryToDatabase(sampleCode)));
criteria.add(Restrictions.isNotNull("container"));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java
index 2e0478030174f9757b104ace09219b66eee77b6a..00626bd8a3cd7dbea8724d8e176d9a017aa322b8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java
@@ -37,6 +37,8 @@ public class SampleIdentifier extends SampleOwnerIdentifier
private String sampleSubCode;
+ private String containerCodeOrNull;
+
private SampleIdentifier(final DatabaseInstanceIdentifier databaseInstanceIdentOrNull,
final SpaceIdentifier spaceIdentOrNull, final String sampleCode)
{
@@ -88,6 +90,11 @@ public class SampleIdentifier extends SampleOwnerIdentifier
return sampleSubCode;
}
+ public String getContainerCodeOrNull()
+ {
+ return containerCodeOrNull;
+ }
+
/**
* Returns an object that only contains the owner information of this sample identifier.
* {@link #hashCode()} will be the same when called on two different samples with same owner.
@@ -111,6 +118,10 @@ public class SampleIdentifier extends SampleOwnerIdentifier
{
String[] sampleCodeTokens = sampleCode.split(CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING);
this.sampleSubCode = sampleCodeTokens[sampleCodeTokens.length - 1];
+ if (sampleCodeTokens.length > 1)
+ {
+ containerCodeOrNull = sampleCodeTokens[0];
+ }
} else
{
this.sampleSubCode = sampleCode;